27 April 2015

Late today, I got notice that it was time to activate my email address for UTRGV.

Done.

It was quick to do, but in many ways, it signaled the end of an era for me.

An institutional email address is central to modern academic life. It is the first point of contact that people look for if they are trying to connect with you. More than office space, building keys, an ID card, or listing on an university website, a .edu email address defines your affiliation with an institution, both to that institution and to the rest of the world.

The UTRGV email drives home for me that UTPA is coming to an end.

Since I practically live online (“Hi, my name is Zen, and I’m a netaholic”), I have made the problem much, much worse for myself. I use my academic email for a lot of online services, and now I will have a long, slow trudge of switching all the profile account information. Updating a single paper in my academic sites took me half a day. I have no idea how long it will be before I swap over all my accounts to my @utrgv.edu email addy.

This is probably a good time to start listing my university affiliation on new manuscripts I submit as “University of Texas Rio Grande Valley,” too.

I have a lot of mixed feelings about this, because I am watching how this institution is developing. And I am not always feeling optimistic about what I see. But maybe that’s another post for another time.

21 April 2015

My field work is on a sandy beach, so there are not very many hard surfaces available for organisms to settle on. So I don’t expect to find these crustaceans when I was at the beach on the weekend...

Barnacles! Some variety of gooseneck barnacle, I reckon, growing on some sort of floating seed (I think). I love that they would just keep extending their feeding legs (cirri, pretty calmly, even though I was holding them out of the water.

Mark worries about “self-funded” doctoral degrees. Is this exploitation? Maybe, but I’m curious about where the line is drawn. Should we be drawing lines in the sand over “self-funded” master’s degrees, particularly with thesis? Undergraduate degrees that are research intensive?

13 April 2015

The lion’s face is perhaps the purest expression of fury I have ever seen. The penguin picture is shocking because it is completely unexpected. It’s also a vivid reminder that birds are the direct descendents of meat-eating dinosaurs.

In our most recent paper on nociception, one of the major points is that not all animals react to potentially nasty stimuli the same way. And it turns out that there’s a very nice demonstration of that idea on Mythbusters. In the 2008 Shark Week “Jawsome Special,” the Mythbusters did a segment called “Spicy Salsa Shark Shield.”

They showed that sharks were not deterred by the presence of capsaicin-laden material.

I took it out, because there were other references that made the point about how responses to noxious stimuli varied from species to species. It wasn’t worth fighting over, and I think I’d have lost.

Regardless of the esteem you hold for the work done by Mythbusters, the journal’s citation policing raises bigger issues. A current trend in academic publishing is to broaden the kinds of research products that people can get academic credit for. Why should only publications “count,” and not sharing a database, or writing useful code?

Consider figshare, the cloud storage data archiving service. One of their big selling points as a data repository is that they generate digital object identifiers (DOI) for stuff submitted there. The DOI itself is not the selling point, but they strongly imply that this makes whatever is archived on Figshare citable in scholarly publications. Here’s the top from their “about” page: making things citable is the first thing the list. (my emphasis):

figshare is a repository where users can make all of their research outputs available in a citable, shareable and discoverable manner.

But all those hopes can be dashed by a single sentence from a journal. “Nope, we only take peer reviewed papers.”

Interestingly, the journal let us keep in a couple of conference abstracts. The abstracts were in published in a peer-reviewed society journal, but the abstracts themselves were not peer-reviewed.

I’ve noted before that some journals have had a tradition of allowing people to cite “grey literature,” like conference abstracts, newspaper articles, web pages, or tweets. I think that is a positive thing. I worry that this sort of “journals citing (and therefore promoting) journals” policy might become more common as journals compete for scientific products. Such policies could hamper the development of academic publishing innovations.

Even worse, a “journal only” policy has the potential to force authors into intellectual dishonesty. “We got this idea from another lab’s data on figshare, but we can’t say that in the paper, so we’ll just have to say something else.”

Authors and possibly reviewers should be determining what is a legitimate citation on a case by case basis, rather than a journal setting a blanket policy favourable to itself.

10 April 2015

To celebrate the outstanding UTPA authors who have published scholarly works or been awarded major research grants in the past year.

It’s next week. I’m not going. There are more interesting things I could do. Trivia night at the pub, the Face-Off finale, cheap movie night... But most importantly, I’m not going because it doesn’t make me feel good about what I achieved.

I got thinking about what makes me feel successful after reading this article in The Chronicle of Higher Education (my emphasis):

For some of us, it’s not that we are afraid to lean in. It’s that we have jumped in head first and are barely treading water even when we are considered “successful.” It’s not that my success has come at the expense of family or that my career advancement has been stifled by raising a family. It’s that my success in academe is simply not the kind of success that I envisioned for myself. Success should feel good, make you beam with pride, feel as if all your hard work was worthy of something bigger. I envisioned, and frankly deserve, a type of success in which the next panic attack isn’t just around the corner and in which supportive spouses don’t feel like they must resort to ultimatums to cultivate a meaningful family life.

An institutional dinner doesn’t make me feel successful. If I go, I’ll just be annoyed.

First, this event isn’t for people who published a lot of papers. Oh no. “Scholarly works” is defined here as books and book chapters. That’s not the major way people in the sciences communicate their work. In fact, book chapters a good way to bury your work in science. So all my colleagues who are kicking ass writing publications... too bad. No dinner for you.

Second, that it includes people who get grants is a reminder of that my institution values money for its own sake, rather than focusing on the new knowledge that we’re supposed to be generating with the money. If you want to reward people who got grants, great. Getting a grant is hard. But don’t call it an “author’s recognition and reception”; call it an “author’s and fundraisers recognition and reception”

Third, how do you get invited to this event? By self identification. The institution can’t even be bothered to check our annual folders, our CVs that I’ve sent forward multiple copies every year, it seems, or the “digital measures” system they put in place to be able to keep track of what people are doing. No, they have to email deans and chairs to ask their faculty, “Who put out a book or a chapter in the last year?”

Nope. That invitation didn’t make me feel “celebrated.” It make me feel like a cog in an institutional public relations machine.

But there was something that made me feel successful recently. It was easy to pick out. My department chair was in the doorway of my office, and we were talking about something, and he said something like, “I noticed that you’ve been kicking ass at research lately.”

That one sentence felt really good.

It felt good because it was personal, face-to-face, from a colleague I like and trust, unsolicited, and not in response to any self-promotion I was doing. That was so much better than any institutional dinner shindig.

09 April 2015

For several unbloggable reasons, I have spent very close to working a traditional 40 hour work week the last few months. This is a pretty substantial cut for me.

And this is the point where everyone wants me to say, “And I’m feeling much better now!”

A lot of people have written about the cult of business in academia, and how there are a lot of bad examples of overwork. A few years ago, one person (Nobel prize winner, I think) talked about how some of his best ideas he got from noodling around in the lab... on Sunday afternoons. He copped it for setting a bad example for unrealistic work expectations. Not everyone can or should spend weekends in the lab.

My feelings about moving to a more “9 to 5” schedule are not that simple.

On the one hand, if I’m honest, I did used to feel that there was nothing in my life but work. That wasn’t very pleasant.

Now, there is more to my life than work, and that’s good. But now I feel crummy about the work I do get done. I’m constantly aware of how many tasks need doing. I’m behind on grading, I’m behind on page proofs, I’m behind on administration, I’m behind on revising manuscripts... and I hate that feeling.

(Oh, and my office is a disaster area.)

Fortunately, this feeling of not getting it done isn’t showing in my productivity on paper yet. I’ve had one paper published that year, pre-prints are out for a second, and severalcontributions for books are in the pipeline for later this year. But I was lucky: I had a lot of projects that had a very long, slow, fuse that are just finally coming out after long delays.

And the things that are suffering are things that I like doing, that make me feel like an academic contributing to the dialogue. It feels so good when I get to blog now. I want to do more. I’m turning down students interesting in research projects, because I know I don’t have the time to give them the attention they deserve. I’ve had to cut myself off a lot in an effort to keep myself focused on the backlog.

I think I may need some time that isn’t the daily 9 to 5 grind of academia (teaching and meetings and writing) but that is still related to it. Maybe that guy was on to something with Sunday afternoons in the lab. Maybe just occasionally.

08 April 2015

Model organisms are great, but as interest has turned to model organisms (particularly genetic ones), we’ve seen less and less attention paid to... the rest of the living world.

A new book series tries to remedy this somewhat for one field: Evolutionary Developmental Biology of Invertebrates. I contributed a little to a chapter in volume 4 with Steffen Harzsch and Jakob Kreiger on development in decapod crustaceans. I just looked at the page proofs recently, and it looks lovely.

Volumes 1, 3, 4, 5, and 6 are listed in the Springer website. I am guessing that there will be a volume 2, and the editor is not pulling some elaborate prank to leave us with non-sequential volumes.

Check out those claws! That’s clearly what it uses to bring the thunder. Myomenippe hardwickii, which the photographer designates as a “thunder crab.”Photo by budak on Flickr; used under a Creative Commons license.

06 April 2015

There is a cottage industry of people who feel the need to show, “There are journals that will publish crap!” And it’s getting tiring.

The Scholarly Kitchen did this to Bentham Journals a few years ago, we had the Bohannon “sting” in Science, the angry “Get me off your fucking mailing list” paper. A recent entry into this pageant is a cocoa puffs paper. A new editorial calls predatory journals “publication pollution.”

To listen to some of these, you could be forgiven for thinking that publishing a paper in one of these journals is practically academic misconduct: a career-ending, unrecoverable event.

I talk to a lot of working scientists, both online and in person. And in all of that time, how many scientists have I heard of who have reported someone who submitted to one of these journals, who were not satisfied with their experience?

Three. One experience is described in two posts (here and here), and a couple of others were tweeted at me when I asked for examples. And two were “my friend” stories, not personal accounts. For the amount of handwringing over predatory publishers, this is a vanishingly small number.

Of course, these numbers are probably under reported, because nobody wants to admit that they published in a junk journal. It’s like admitting you got taken in by an email from someone claiming to be a Nigerian prince. It’s embarrassing to admit when you should have known better.

Let’s say that someone pays and publishes a paper in a predatory journal. Who is harmed, how much are they harmed, and what recourse is there to address the harm?

The author

An author who publishes in such a journal has paid the article processing charge. Okay, that sucks. But presumably the author knew she or he was going to be getting an invoice, and would not have gone that route if she or he was utterly unable to pay.

Assuming that the author has not gone into great financial hardship, let’s say the paper is published online, but without proper peer review. What are the possible outcomes, and what harms might arise?

If the paper is competent, the author could harmed because people will not read the paper because of the journal. But the paper is available for other researchers can use it and cite it if they so choose. People cite non-reviewed stuff all the time (conference abstracts, non journal articles).

If an author realizes that this was a non-peer reviewed venue, what can she or he do about it? The author can try to retract it. If the journal does not, the author can try to publish it elsewhere. Real journal editors might be sympathetic to the plight of authors who made a mistake in the publishing venue.

Ultimately, I don’t see severe harm done to an honest author who publishes in the wrong journal. It’s reasonable to ask if that harm couldn’t have been avoided with a little due diligence. Authors should know the principle “Caveat emptor” applies as much to journals as other services.

The public

Another argument is that the harm of publishing in predatory journals is that the public or the unwary will be confused, because the findings could be untrue. Let’s examine a few scenarios of how findings could be false.

The research was not done well. This is no different from research published in other journals. There are many, many cases of research that was poorly done, but published anyway. This is why post-publication peer review is important. This is why replication is important. Scientists perform post-publication peer review all the time. It is our job. This is what we do.

The researchers are malicious. It is possible that someone with an agenda might try to give dubious information some sort of veneer of respectability by publishing it in a predatory journal. But... why? There are many easier ways for people with an agenda to spread lies than publishing in a crummy journal.

Professional climate denier Marc Morano has never published a scientific article. Neither has dubious diet critic the Food Babe. They don’t need to, when they’ve found so many media platforms that give them a so much bigger audience. It’s not clear how an article in a junk journal is supposed to be a more effective way of spreading untrue information than a blog, or an infomercial, appearing on a cable news network sympathetic to certain ideas and ideologies, or any of the other hundreds of ways people can spread lies.

This raises the question of how the general public finds out about research of any sort, including the dodgy stuff. Most members of the general public are not scouring academic journals. For there to be significant spread of the false research findings, it would either have to be spread through the general media or social media

General media. Science journalists who have any baseline competence should understand scientific publishing enough to realize that not every research article in every scientific journal is true. Publishing in a little known journal should raise an immediate red flag and warrant investigation before filing a story. If any journalist doesn’t do that, you have “churnalism,” and in my mind, that’s a separate – and much bigger – problem than a junk journal.

Social media. So far, I know of no cases where an article from an alleged “predatory” journal has gone viral. But let’s say it does. One of the powers of social media is that if something does go viral, it gets a lot of attention, including relevant experts can talk about it. They are probably going to comment, and be asked to comment, and can explain why such and such a paper is problematic. One of the wonderful things about the dress was that it gave lots of experts a chance to explain what we know about visual system.

Other scientists

I am not sure I see much potential harm for other scientists if a paper is published in a crappy journal. Because the entire point of a journal being called “predatory” is a way of saying that it has no standing in the scientific community. So if a journal is already being ignored by a scientific community, how is it going supposed to affect that community?

Evaluating articles is what we working professional are supposed to be doing. Like, all the time. I suppose that there is a minor harm in that people might have an opportunity cost in time spent debunking papers in junk journals. But more likely, papers in bogus journals are going to suffer the same fate as a lot of other articles: they’ll just be ignored.

Another argument might be that the general scientific community is harmed because there is reduced public trust in science. As I outlined above, I can’t see that happening.

The major reasons that scientists get their panties in a bunch about predatory journals is not because junk “predatory” have done much demonstrable harm to anyone, other than authors who are out their processing fees. I see lots hand waving about the “purity and integrity of the scientific record,” which is never how it’s been. The scientific literature has always been messy. We always have verify, replicate, and often correct published results.

“The danger of this model is that upfront fees provide short term incentives for journals to accept papers from anyone who has the money to pay, regardless of their scientific value or accuracy.” Is there any evidence that this is a serious risk? As the author himself notes, no journal will build a reputation for quality by publishing any old rubbish. This is a bit of a straw man argument.

Some people have claimed that these predatory journals exploit scientists in developing countries. It reminds me a little of someone on Twitter who recounted asking at a historical tour, “Were slaves kept here?” The guide answered, “Yes, they had good houses and were well cared for.” The problem wasn’t whether they had decent housing, the problem was they were slaves.

The problems for researchers in developing countries are not predatory journals. The problems that such researchers have is bad infrastructure, lack of support, and poor mentoring that prevents them from putting together papers that could be published in mainstream scientific journals. That they may be working under incentives that do not reward them for discriminating between journals. I also am waiting to hear from the waves of dissatisfied scientists from developing countries who feel they got ripped off.

I also noticed this when I tried to read a new entry in the “OMG predatory journals” collection:

It’s not quite an open access irony award winner... but it’s close. You want to complain about scientific publishing? Let’s talk about the regular, routine obstruction to reading the scientific literature that occurs even a professional working scientist at an expanding university with ever increasing research expectations. That affects routinely me, in a way predatory journals never have.

Open access is a new business model. Who benefits from constantly crying wolf on “predatory” journals? Established journals from established publishers, whose business model includes, in part, in asking over US$30 to read an editorial.

We should be worried about parasites as well as predators in the scientific publishing ecosystem.

Additional, 8 April 2015: There is a little bit of data indicating that these junk journals are not being read here. Hat tip to Lenny Teytelman.